Laurence des Cars tendered her resignation, which Macron accepted, "praising an act of responsibility at a time when the world's largest museum needs calm and a strong new impetus to successfully carry out major projects involving security and modernisation", his office said.
Des Cars has faced intense criticism since burglars made off in October with jewels worth an estimated $A145 million that are still missing, exposing glaring security gaps at the world's most-visited museum.
Strikes over pay and conditions since December have also led to regular closures and added to a list of woes that included two water leaks as well as a massive ticket fraud investigation.
Critics including the state auditors' office have questioned the museum's low spending on security and infrastructure maintenance while it made lavish purchases of new artwork, only a quarter of which is open to the public, and spent heavily on post-pandemic relaunch projects.
Macron wants to give des Cars a new mission during France's presidency of the Group of Seven leading industrialised nations, focused on cooperation among major museums, the statement said.
For many in France's cultural world, the resignation answers months of head-scratching over why no top official had fallen after the heist: a daylight robbery that many here saw as the most humiliating breach of French heritage security in living memory.
Thieves took less than eight minutes to steal the crown jewels in a weekend operation that stunned visitors, exposed glaring vulnerabilities and left one of France's most symbolically charged collections in criminal hands.
Several suspects were later arrested, but the stolen pieces remain missing.
Des Cars, one of the most prominent museum directors in Europe, had reportedly offered to resign on the day of the robbery, but it was initially refused by the culture minister.
In remarks after the theft, she described the moment as a "tragic, brutal, violent reality" for the Louvre and said that, as the person in charge, it had felt right to offer her resignation.
with AP
